graeme ball dundee microscopy image analyst

Graeme Ball

Dundee Microscopy Image Analyst

Lesterlin C, Ball G, Schermelleh L, Sherratt DJ. RecA bundles mediate homology pairing between distant sisters during DNA break repair. Nature (2013) doi: 10.1038/nature12868.

ImageJ: e.g. 3D Quantification

• ImageJ and ImageJ scripts are very versatile

• Typical example of ImageJ macros I write:

quantify intensity in a 3D region defined by a

marker channel

Studying Cell Polarity: MATLAB Tracker

(MATLAB for interactive data analysis, prototyping)

1. MATLAB tracking tool for growing MT +ends (EB1)

Studying Cell Polarity: MATLAB Tracker

1. MATLAB tracking tool for growing MT +ends (EB1)

Studying Cell Polarity: directionality stats

2. “ParticleStats” extended to summarise directionality

Parton RM, Hamilton RS, Ball G, Yang L, Cullen CF, Lu W, Ohkura H, Davis I. A PAR-1-ependent orientation gradient of dynamic microtubules directs posterior cargo transport in the Drosophila oocyte. JCB 2011; 194(1):121-135.

MicrobeTracker Extensions to Study DNA DSB Repair

Lesterlin C, Ball G, Schermelleh L, Sherratt DJ. RecA bundles mediate homology pairing between distant sisters during DNA break repair. Nature (2013) doi: 10.1038/nature12868.

OMERO Scripts for Batch Processing

SIMcheck ImageJ Plugin Suite for SIM Data

Have Set up Analysis Suite & Web / Booking

ImageJ Volocity softWoRx Imaris

CellProfiler MATLAB

Plan for Image Analysis Support

● software &

computing

● advice

● training & teaching

● collaborations

Working with python API: Feedback

• Documentation is better than it used to be

• A lot of complexity (Ice, model), not well-

hidden

• Blitz gateway awkward / verbose to use (&

lazy)

• Eventually found useful bits & pieces outside

Blitz:-lib/python/omeroweb/webclient/controller/container.py

lib/python/omeroweb/webclient/webclient_gateway.py

lib/python/omero/util/script_utils.py

(often after writing the same things myself…)

• No python client, just the whole server.

OMERO seems useful to me as…

• Image repository: secure, viewable, searchable

• Collaborative work tool: sharing data, comments,

tags

• Batch processor: non-interactive jobs, simple

interface

• Image repository: secure, viewable, searchable

• Collaborative work tool: sharing data,

comments, tags

• Batch processor: non-interactive jobs, simple

interface

Wish list / questions

1. Tidy the interface: find features in seconds, less clicks.

1. Share like Dropbox: *user* can search and add contacts

1. Run processing jobs on a node other than the server (√?)

2. Fix search: like google, search all (incl. filename, metadata).

2. Collaborative tagging (sets), comments (√), messages/inbox.

2. Improve python API / docs: simpler, higher level.

7. Export projects / desktop sync / revision history (!)

3. More content: protocols, references, figures.

3. Queue management functionality, job status.For now, we will try to achieve this by setting up research groups and a Public group

• Let the web app & insight diverge:

- web for collaborative, admin, job

management

- insight for Desktop integration (e.g. IJ),

sync?

• Fiji update site?

Finally,

Questions?